The invention concerns the use of duplex oligonucleobase compounds (hereafter xe2x80x9cduplex mutational vectorsxe2x80x9d) to specifically make alterations in the sequence of a DNA in a cell. In one embodiment the invention concerns compounds and methods of their use to make specific genetic alterations in the genome and in episomes (plasmids) of target prokaryotic cells. In a further embodiment the invention concerns methods of using bacterial cells to develop more efficient duplex mutational vectors. The structure of the duplex mutational vector (DMV) is designed so that genetic exchange between the DMV and the target gene occurs, i.e., a sequence contained in the DMV replaces the sequence of the target gene. In still further embodiments the invention concerns specific generic structures of DMV.
U.S. Pat. No. 5,565,350, issued Oct. 15, 1996, and U.S. Pat. No. 5,731,181, issued Mar. 24, 1998 by E. B. Kmiec, described Chimeric Mutational Vectors (CMV), i.e., vectors having both DNA-type and RNA-type nucleobases for the introduction of genetic changes in eukaryotic cells. Such CMV were characterized by having at least 3 contiguous base pairs wherein DNA-type and RNA-type nucleobases are Watson-Crick paired with each other to form a hybrid-duplex. A CMV designed to repair a mutation in the gene encoding liver/bone/kidney type alkaline phosphatase was reported in Yoon, K., et al., March 1996, Proc. Natl. Acad. Sci. 93, 2071. The alkaline phosphatase gene was transiently introduced into CHO cells by a plasmid. Six hours later the CMV was introduced. The plasmid was recovered at 24 hours after introduction of the CMV and analyzed. The results showed that approximately 30 to 38% of the alkaline phosphatase genes were repaired by the CMV.
A CMV designed to correct the mutation in the human xcex2-globin gene that causes Sickle Cell Disease and its successful use was described in Cole-Strauss, A., et al., 1996, Science 273:1386. A CMV designed to create a mutation in a rat blood coagulation factor IX gene in the hepatocyte of a rat is disclosed in Kren et al., 1998, Nature Medicine 4, 285-290. An example of a CMV having one base of a first strand that is paired with a non-complementary base of a second strand is shown in Kren et al., June 1997, Hepatology 25, 1462.
U.S. patent application Ser. No. 08/640,517, filed May 1, 1996 now U.S. Pat. No. 5,760,012, by E. B. Kmiec, A. Cole-Strauss and K. Yoon, published as WO97/41141, Nov. 6, 1997, and application Ser. No. 08/906,265 now U.S. Pat. No. 5,888,983, filed Aug. 5, 1997, disclose methods and CMV that are useful in the treatment of genetic diseases of hematopoietic cells, e.g., Sickle Cell Disease, Thalassemia and Gaucher Disease.
The above-cited scientific publications of Yoon, Cole-Straauss and Kren describe CMV having two 2xe2x80x2-O-methyl RNA segments separated by an intervening DNA segment, which were located on the strand opposite the strand having the 5xe2x80x2 end nucleotide. U.S. Pat. No. 5,565,350 described a CMV having a single segment of 2xe2x80x2-O-methylated RNA, which was located on the chain having the 5xe2x80x2 end nucleotide. An oligonucleotide having complementary deoxyribonucleotides and a continuous segment of unmodified ribonucleotides on the strand opposite the strand having the 5xe2x80x2 end nucleotide was described in Kmiec, E. B., et al., 1994, Mol. and Cell. Biol. 14:7163-7172. The sequence of the strand was derived from the bacteriophage M13mp19,
The use of single stranded oligonucleotides to introduce specific mutations in yeast are disclosed in Yamamoto, T., et al., 1992, Genetics 131, 811-819. The oligonucleotides were between about 30 and 50 bases. Similar results were reported by Campbell, C. R., et al., 1989, The New Biologist, 1, 223-227. Duplex DNA fragments of about 160 base pairs in length have been reported to introduce specific mutations in cultured mammalian cells. Hunger-Bertling, K., et al., 1990, Molecular and Cellular Biochemistry 92, 107-116.
Applicants are aware of the following provisional applications that contain teaching with regard to uses and delivery systems of recombinagenic oligonucleotides: By Steer et al., Ser. Nos. 60/045,288 filed Apr. 30, 1997; 60/054,837 filed Aug. 5,1997; 60/064,996, filed Nov. 10, 1997; and by Steer and Roy-Chowdhury et al., Ser. No. 60/074,497, filed Feb. 12, 1998, entitled xe2x80x9cMethods of Prophylaxis and Treatment by Alteration of APO B and APO E Genes.xe2x80x9d